From: Daniel Barton <daluke.barton@gmail.com>
Date: Tue, 27 Aug 2013 12:47:23 +0000 (+0100)
Subject: JAL-1358 Just the eclipse project/classpath files so that I can stash changes and... 
X-Git-Tag: Jalview_2_9~200^2~21^2~22
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c7aec7d18ae7567c160be71b318139a9aa2b1c32;p=jalview.git

JAL-1358 Just the eclipse project/classpath files so that I can stash changes and demonstrate DisorderAnnotExportImport failure
---

diff --git a/.classpath b/.classpath
index f396252..8f6f94c 100644
--- a/.classpath
+++ b/.classpath
@@ -39,7 +39,6 @@
 	<classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
 	<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
 	<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
-	<classpathentry kind="lib" path="lib/min-jaba-client-2.0.jar" sourcepath="/clustengine2"/>
 	<classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
 	<classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
 	<classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
@@ -48,5 +47,6 @@
 	<classpathentry kind="lib" path="lib/VARNAv3-9-dev.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
+	<classpathentry kind="lib" path="lib/rnaalifold-jaba-dan-test3.jar"/>
 	<classpathentry kind="output" path="classes"/>
 </classpath>
diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
new file mode 100644
index 0000000..70ddb7e
--- /dev/null
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -0,0 +1,140 @@
+package jalview.ws.jws2;
+
+import jalview.api.AlignCalcWorkerI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.gui.AlignFrame;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.TreeSet;
+
+import compbio.data.msa.jaxws.Align;
+import compbio.data.sequence.Range;
+import compbio.data.sequence.Score;
+import compbio.data.sequence.RNAStructScoreManager;
+import compbio.data.sequence.ScoreManager;
+import compbio.metadata.Argument;
+
+public class RNAalifoldClient extends JabawsAlignCalcWorker implements
+		AlignCalcWorkerI 
+{
+	
+	String methodName;
+	
+	AlignFrame af;
+	
+	public RNAalifoldClient(Jws2Instance sh, AlignFrame alignFrame,
+			WsParamSetI preset, List<Argument> paramset)
+	{
+		super(sh, alignFrame, preset, paramset);
+
+		
+		af = alignFrame;
+				
+		methodName = sh.serviceType;
+
+	}
+	
+	 @Override
+	  public String getServiceActionText()
+	  {
+	    return "Submitting RNA alignment for Secondary Structure prediction using"
+	    		+ "RNAalifold Service";
+	  }
+	
+	@Override
+	public void updateResultAnnotation(boolean immediate)
+	{
+
+		if (immediate || !calcMan.isWorking(this) && scoremanager != null) 
+		{
+			
+
+			
+			List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+//			ourAnnots = new ArrayList<AlignmentAnnotation>();
+
+			// So I don't have to do any more casting
+			List<String> structs = ((RNAStructScoreManager) scoremanager).getStructs();
+			List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager).getData();
+			
+			// Deal with the consensus structure and (?)BasePair Probabilities
+			Annotation[] anns = new Annotation[structs.get(1).length()];
+
+			// check if the first Score object is populated with base pair probabilities
+			Score fscore = data.get(0).first();
+			boolean BPScores = (fscore.getScores().size() > 0 
+					&& fscore.getRanges() != null);
+
+			TreeMap<Range, Float> basePairs = null;
+			if (BPScores) {
+				// The base pair probabilities are stored in a set in scoremanager... we want a map
+				basePairs = new TreeMap<Range, Float>();
+				for (Score score : data.get(0)) {
+					// The Score objects contain a set of size one containing the range and
+					//  an ArrayList<float> of size one containing the probabilty
+					basePairs.put(score.getRanges().first(), new Float(score.getScores().get(0)));
+				}
+			}
+
+			// ignoring the Consensus alignemnt for now, get the Structure and make an AlignmentAnnotation
+			String struct = structs.get(1);
+			for (int i = 0; i < struct.length(); i++) {
+
+				if (BPScores) {
+					// Return all the contacts associated with position i
+					List<Range> contacts = isContact(basePairs, i+1);
+
+					if (contacts.size() == 0) {
+						anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), 0f);
+					}
+					else if (contacts.size() == 1) {
+						// There is only one contact associated with this base
+						float prob = basePairs.get(contacts.get(i));
+						anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), prob);
+					}
+					else if (contacts.size() > 1) {
+						// For now we will simply deal with alternate contact information by mentioning its
+						//  existance in the description
+						float prob = basePairs.get(contacts.get(i));
+						anns[i] = new Annotation(struct.substring(i, i+1), "This base has alternate contact(s)",
+								struct.charAt(i), prob);
+					}
+				}
+				else {
+					// Same as the first if from the previous block
+					anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), 0f);
+				}
+			}
+			
+			AlignmentAnnotation annot = new AlignmentAnnotation("Consensus Structure", "Free Energy", anns);
+			annot.setScore(data.get(1).first().getScores().get(0));
+
+			if (ourAnnot.size() > 0) {
+				updateOurAnnots(ourAnnot);
+			}
+
+		}
+	}
+	
+	// Check whether, at position i there is a base contact and return all the
+	//  contacts at this position. Should be in order of descending probability.
+	private List<Range> isContact(TreeMap<Range, Float> basePairs, int i) {
+		
+		List<Range> contacts = new ArrayList<Range>();
+		
+		for (Range contact : basePairs.keySet()) {
+			// finds the contacts associtated with position i ordered by the natural
+			//  ordering of the Scores TreeSet in ScoreManager which is, descending probability
+			if (contact.from == i || contact.to == i) contacts.add(contact);
+		}
+		
+		return contacts;
+	}
+}